In order to assist in the use of cats as disease models, a feline fosmid library was developed by Agencourt (Beverly, MA) containing over 600,000 fosmid clones were sequenced from both ends using primers flanking the 40 kb inserts and included in the 2X draft domestic cat genome sequence (Agencourt, Beverly, MA and the Broad Institute, Boston, MA). These two resources (fosmid library and draft genome sequence) provide a means to finish regions of the cat genome that are missing in the draft sequence. In recent years, a variety of host restriction genes have been identified in humans and mammals that modulate retrovirus infectivity, replication, assembly and/or cross-species transmission. One of these host encoded genes, Apolipoprotein B mRNA-editing enzyme catalytic (APOBEC3) is capable of terminally editing feline foamy virus in the absence virally-encoded Bet protein, but not in its presence similar to the interplay of APOBEC3 and the HIV encoded protein Vif (Lochelt, et al., 2005). The editing capacity of APOBEC3 gene products appears to be species specific and is thought to restrict cross-species transmission of retroviruses. To identify and characterize APOBEC genes in the feline genome, we first identified APOBEC related sequences in the scaffolds of the partial (2x) genome sequence of the domestic cat and compared these phylogenetically to their human and dog counterparts. This analysis showed that the domestic cat contains homologues for APOBEC1, APOBEC 2, APOBEC 3 (three genes defined as 3A, 3B and 3H -the latter formerly known as ARP10), and APOBEC 4. However, none of these were identical to the previously published cat APOBEC3 cDNA nor were the APOBEC3 genes located on the same scaffold sequence indicating sequence gaps. After organizing the fosmid database for targeted sequencing of the selected fosmid clones, we isolated a set of 10 fosmid clones predicted on the basis of the location of their end sequence relative to the scaffolds sequence to either contain or flank at least one of the APOBEC3 gene(s). These were analyzed by PCR using primers designed to distinguish between cat APOBEC3A, 3B, and 3H and a total of five fosmid clones were positive for one or more of these genes. Two of these fosmids were then sequenced using transposon insertions and subsequent analysis revealed that one fosmid contained the complete gene for cat APOBEC3A, and the other contained four APOBEC3 genes including APOBEC3B and 3H.